diff --git a/subworkflows/local/workflows.nf b/subworkflows/local/workflows.nf index d7fdcfe..883f4ca 100644 --- a/subworkflows/local/workflows.nf +++ b/subworkflows/local/workflows.nf @@ -314,8 +314,8 @@ workflow VC { | map{samplename,marked,markedindex,normvcf,normindex -> tuple(samplename.split('_vs_')[0],samplename.split('_vs_')[1],"octopus",normvcf,normindex)} annotvep_tn_octopus(octopus_in) - octopus_in_sc = octopus_in | octopus_convertvcf - | map{tumor,vcf,vcfindex ->tuple(tumor,"octopus_tonly",normvcf,normindex)} + octopus_in_sc = octopus_in | octopus_convertvcf + | map{tumor,normal,vcf,vcfindex ->tuple(tumor,normal,"octopus",vcf,vcfindex)} //Octopus TOnly octopus_in_tonly=bambyinterval.map{tumor,bam,bai,normal,nbam,nbai,bed-> @@ -327,10 +327,10 @@ workflow VC { map{tumor,marked,markedindex,normvcf,normindex,normal ->tuple(tumor,"octopus_tonly",normvcf,normindex)} annotvep_tonly_octopus(octopus_in_tonly) octopus_in_tonly_sc=octopus_in_tonly | octopus_convertvcf_tonly - | map{tumor,vcf,vcfindex ->tuple(tumor,"octopus_tonly",normvcf,normindex)} + | map{tumor,vcf,vcfindex ->tuple(tumor,"octopus_tonly",vcf,vcfindex)} //Combine All Variants Using VCF and Then Reannotate - mutect2_in|concat(strelka_in)|concat(octopus_in_sc)|concat(muse_in)|concat(lofreq_in) + mutect2_in|concat(strelka_in) | concat(octopus_in_sc) | concat(muse_in) | concat(lofreq_in) | concat(vardict_in) |concat(varscan_in) | groupTuple(by:[0,1]) | somaticcombine | map{tumor,normal,vcf,index ->tuple(tumor,normal,"combined",vcf,index)}